# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 04:17:25 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (~{Z})-3-[2-(naphthalen-2-ylmethyl)phenyl]-2-sulfanyl-prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)/C(S)=C/c1ccccc1Cc2ccc3ccccc3c2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CF8  CF8  '(~{Z})-3-[2-(naphthalen-2-ylmethyl)phenyl]-2-sulfanyl-prop-2-enoic acid'  ligand  39  23  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CF8
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CF8  C4   C  CR16  0  -0.275  -2.3932  -2.2020   0.8193
 CF8  C5   C  CR16  0  -0.257  -2.3394  -3.5859   0.9108
 CF8  C6   C  CR16  0  -0.246  -1.5660  -4.3035   0.0109
 CF8  C7   C  CR16  0  -0.318  -0.8539  -3.6348  -0.9773
 CF8  C8   C  CR6   0   0.127  -0.9073  -2.2512  -1.0886
 CF8  C9   C  CH2   0  -0.591  -0.1200  -1.5245  -2.1461
 CF8  C10  C  CR6   0   0.118   0.8524  -0.5201  -1.5722
 CF8  C11  C  CR16  0  -0.351   1.6509  -0.8366  -0.5037
 CF8  C12  C  CR66  0   0.158   2.5429   0.1061   0.0537
 CF8  C13  C  CR16  0  -0.315   3.3665  -0.2084   1.1606
 CF8  C14  C  CR16  0  -0.261   4.2149   0.7264   1.6879
 CF8  C15  C  CR16  0  -0.263   4.2807   2.0231   1.1336
 CF8  C    C  C     0  -0.240  -1.4313   0.8322   0.6355
 CF8  O    O  OH1   0  -0.594  -1.2229   3.0491   1.3216
 CF8  C1   C  C     0   0.567  -1.6136   2.2743   0.3221
 CF8  C16  C  CR16  0  -0.312   3.4957   2.3552   0.0631
 CF8  C17  C  CR66  0   0.102   2.6104   1.4084  -0.5030
 CF8  C18  C  CR16  0  -0.300   1.7852   1.7146  -1.6094
 CF8  C19  C  CR16  0  -0.303   0.9368   0.7772  -2.1277
 CF8  C3   C  CR6   0   0.001  -1.6861  -1.5273  -0.1735
 CF8  O1   O  O     0  -0.432  -2.0716   2.6932  -0.7119
 CF8  S    S  S2    0  -0.130  -0.7001   0.4882   2.2005
 CF8  H1   H  HCR6  0   0.263  -3.0016  -1.6391   1.5167
 CF8  H2   H  HCR6  0   0.259  -2.8980  -4.0983   1.6829
 CF8  H3   H  HCR6  0   0.259  -1.5119  -5.3824   0.0778
 CF8  H4   H  HCR6  0   0.255  -0.2435  -4.1991  -1.6722
 CF8  H5   H  HCH2  0   0.280   0.4181  -2.2519  -2.7595
 CF8  H6   H  HCH2  0   0.268  -0.8038  -1.0072  -2.8270
 CF8  H7   H  HCR6  0   0.242   1.5993  -1.8256  -0.0601
 CF8  H8   H  HCR6  0   0.249   3.3156  -1.2037   1.5860
 CF8  H9   H  HCR6  0   0.255   4.8396   0.4758   2.5355
 CF8  H10  H  HCR6  0   0.255   4.9565   2.7527   1.5604
 CF8  H11  H  HOH1  0   0.490  -1.3568   3.9824   1.0973
 CF8  H12  H  HCR6  0   0.252   3.5433   3.3504  -0.3630
 CF8  H13  H  HCR6  0   0.249   1.8269   2.7085  -2.0390
 CF8  H14  H  HCR6  0   0.248   0.3021   1.0315  -2.9686
 CF8  H15  H  H     0   0.287  -2.1168   0.3242  -1.2475
 CF8  H16  H  HSH1  0   0.236  -0.3948  -0.7910   1.9529
 CF8  C2   C  C1    0  -0.229  -1.7733  -0.0662  -0.2941

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 CF8  C4   C5   aromatic  1.388  0.020  1.388
 CF8  C4   C3   aromatic  1.393  0.020  1.393
 CF8  C5   C6   aromatic  1.387  0.020  1.387
 CF8  O1   C1   double    1.206  0.020  1.206
 CF8  C6   C7   aromatic  1.390  0.020  1.390
 CF8  C3   C2   single    1.469  0.020  1.469
 CF8  C3   C8   aromatic  1.403  0.020  1.403
 CF8  C2   C    double    1.337  0.020  1.337
 CF8  C1   C    single    1.487  0.020  1.487
 CF8  C1   O    single    1.324  0.020  1.324
 CF8  C16  C15  aromatic  1.368  0.020  1.368
 CF8  C16  C17  aromatic  1.414  0.020  1.414
 CF8  C18  C17  aromatic  1.414  0.020  1.414
 CF8  C18  C19  aromatic  1.366  0.020  1.366
 CF8  C    S    single    1.761  0.020  1.761
 CF8  C7   C8   aromatic  1.389  0.020  1.389
 CF8  C8   C9   single    1.505  0.020  1.505
 CF8  C15  C14  aromatic  1.412  0.020  1.412
 CF8  C17  C12  aromatic  1.418  0.020  1.418
 CF8  C19  C10  aromatic  1.414  0.020  1.414
 CF8  C14  C13  aromatic  1.368  0.020  1.368
 CF8  C12  C11  aromatic  1.412  0.020  1.412
 CF8  C12  C13  aromatic  1.415  0.020  1.415
 CF8  C10  C11  aromatic  1.371  0.020  1.371
 CF8  C10  C9   single    1.511  0.020  1.511
 CF8  C4   H1   single    0.930  0.020  1.080
 CF8  C5   H2   single    0.930  0.020  1.080
 CF8  C6   H3   single    0.930  0.020  1.080
 CF8  C7   H4   single    0.930  0.020  1.080
 CF8  C9   H5   single    0.970  0.020  1.090
 CF8  C9   H6   single    0.970  0.020  1.090
 CF8  C11  H7   single    0.930  0.020  1.080
 CF8  C13  H8   single    0.930  0.020  1.080
 CF8  C14  H9   single    0.930  0.020  1.080
 CF8  C15  H10  single    0.930  0.020  1.080
 CF8  O    H11  single    0.850  0.020  0.980
 CF8  C16  H12  single    0.930  0.020  1.080
 CF8  C18  H13  single    0.930  0.020  1.080
 CF8  C19  H14  single    0.930  0.020  1.080
 CF8  C2   H15  single    0.930  0.020  1.080
 CF8  S    H16  single    1.200  0.020  1.300

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CF8  H1   C4   C3   119.48  3.000
 CF8  H1   C4   C5   119.84  3.000
 CF8  C3   C4   C5   120.68  3.000
 CF8  H2   C5   C6   120.39  3.000
 CF8  H2   C5   C4   119.94  3.000
 CF8  C6   C5   C4   119.66  3.000
 CF8  H3   C6   C7   119.87  3.000
 CF8  H3   C6   C5   120.24  3.000
 CF8  C7   C6   C5   119.89  3.000
 CF8  H4   C7   C8   119.28  3.000
 CF8  H4   C7   C6   119.61  3.000
 CF8  C8   C7   C6   121.10  3.000
 CF8  C3   C8   C9   119.97  3.000
 CF8  C9   C8   C7   121.13  3.000
 CF8  C3   C8   C7   118.89  3.000
 CF8  H6   C9   H5   105.83  3.000
 CF8  H6   C9   C10  108.90  3.000
 CF8  H5   C9   C10  109.79  3.000
 CF8  H6   C9   C8   109.78  3.000
 CF8  H5   C9   C8   109.30  3.000
 CF8  C10  C9   C8   112.99  3.000
 CF8  C19  C10  C11  118.90  3.000
 CF8  C11  C10  C9   121.15  3.000
 CF8  C19  C10  C9   119.94  3.000
 CF8  H7   C11  C12  118.49  3.000
 CF8  H7   C11  C10  120.09  3.000
 CF8  C12  C11  C10  121.42  3.000
 CF8  C17  C12  C13  118.92  3.000
 CF8  C13  C12  C11  121.87  3.000
 CF8  C17  C12  C11  119.22  3.000
 CF8  H8   C13  C14  120.36  3.000
 CF8  H8   C13  C12  118.94  3.000
 CF8  C14  C13  C12  120.71  3.000
 CF8  H9   C14  C15  119.55  3.000
 CF8  H9   C14  C13  120.11  3.000
 CF8  C15  C14  C13  120.34  3.000
 CF8  H10  C15  C16  120.21  3.000
 CF8  H10  C15  C14  119.57  3.000
 CF8  C16  C15  C14  120.22  3.000
 CF8  S    C    C2   126.35  3.000
 CF8  S    C    C1   115.31  3.000
 CF8  C2   C    C1   118.27  3.000
 CF8  H11  O    C1   110.37  3.000
 CF8  O1   C1   O    123.80  3.000
 CF8  O    C1   C    111.86  3.000
 CF8  O1   C1   C    124.34  3.000
 CF8  H12  C16  C17  119.00  3.000
 CF8  H12  C16  C15  120.35  3.000
 CF8  C17  C16  C15  120.65  3.000
 CF8  C18  C17  C16  122.25  3.000
 CF8  C18  C17  C12  118.58  3.000
 CF8  C16  C17  C12  119.17  3.000
 CF8  H13  C18  C19  120.18  3.000
 CF8  H13  C18  C17  119.11  3.000
 CF8  C19  C18  C17  120.71  3.000
 CF8  H14  C19  C18  119.80  3.000
 CF8  H14  C19  C10  119.03  3.000
 CF8  C18  C19  C10  121.17  3.000
 CF8  C2   C3   C8   119.52  3.000
 CF8  C8   C3   C4   119.78  3.000
 CF8  C2   C3   C4   120.68  3.000
 CF8  H16  S    C     96.72  3.000
 CF8  H15  C2   C3   116.65  3.000
 CF8  H15  C2   C    116.72  3.000
 CF8  C3   C2   C    126.59  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CF8  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 CF8  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 CF8  CONST_03  C8   C3   C4   C5      0.00   0.0  0
 CF8  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 CF8  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 CF8  CONST_06  C3   C8   C7   C6      0.00   0.0  0
 CF8  CONST_07  C17  C18  C19  C10     0.00   0.0  0
 CF8  CONST_08  C17  C12  C11  C10     0.00   0.0  0
 CF8  CONST_09  C13  C12  C11  C10   180.00   0.0  0
 CF8  CONST_10  C16  C17  C12  C11   180.00   0.0  0
 CF8  CONST_11  C18  C17  C12  C11     0.00   0.0  0
 CF8  CONST_12  C14  C13  C12  C11   180.00   0.0  0
 CF8  CONST_13  C18  C19  C10  C11     0.00   0.0  0
 CF8  CONST_14  C15  C16  C17  C12     0.00   0.0  0
 CF8  CONST_15  C19  C18  C17  C12     0.00   0.0  0
 CF8  CONST_16  C19  C10  C11  C12     0.00   0.0  0
 CF8  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 CF8  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 CF8  CONST_19  C16  C17  C12  C13     0.00   0.0  0
 CF8  CONST_20  C18  C17  C12  C13   180.00   0.0  0
 CF8  CONST_21  C17  C16  C15  C14     0.00   0.0  0
 CF8  CONST_22  C17  C12  C13  C14     0.00   0.0  0
 CF8  CONST_23  C18  C17  C16  C15   180.00   0.0  0
 CF8  CONST_24  C19  C18  C17  C16   180.00   0.0  0
 CF8  CONST_25  C9   C8   C3   C4    180.00   0.0  0
 CF8  CONST_26  C2   C3   C4   C5    180.00   0.0  0
 CF8  CONST_27  C9   C8   C7   C6    180.00   0.0  0
 CF8  CONST_28  C2   C3   C8   C7    180.00   0.0  0
 CF8  CONST_29  C18  C19  C10  C9    180.00   0.0  0
 CF8  CONST_30  C12  C11  C10  C9    180.00   0.0  0
 CF8  CONST_31  H3   C6   C5   C4    180.00   0.0  0
 CF8  CONST_32  H4   C7   C6   C5    180.00   0.0  0
 CF8  CONST_33  H1   C4   C5   C6    180.00   0.0  0
 CF8  CONST_34  H2   C5   C6   C7    180.00   0.0  0
 CF8  CONST_35  H13  C18  C19  C10   180.00   0.0  0
 CF8  CONST_36  H8   C13  C12  C11     0.00   0.0  0
 CF8  CONST_37  H14  C19  C10  C11   180.00   0.0  0
 CF8  CONST_38  H12  C16  C17  C12   180.00   0.0  0
 CF8  CONST_39  H9   C14  C13  C12   180.00   0.0  0
 CF8  CONST_40  H10  C15  C14  C13   180.00   0.0  0
 CF8  CONST_41  H7   C11  C12  C13     0.00   0.0  0
 CF8  CONST_42  H11  O    C1   C     180.00   0.0  0
 CF8  Var_01    C10  C9   C8   C7   -120.92  30.0  2
 CF8  Var_02    C19  C10  C9   C8   -134.11  30.0  2
 CF8  Var_03    C    C2   C3   C4     60.09  30.0  2
 CF8  Var_04    C3   C2   C    C1   -179.20   0.0  2
 CF8  Var_05    C2   C    C1   O    -179.33  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CF8  plan-1  C4   0.020
 CF8  plan-1  C5   0.020
 CF8  plan-1  C6   0.020
 CF8  plan-1  C7   0.020
 CF8  plan-1  C8   0.020
 CF8  plan-1  C9   0.020
 CF8  plan-1  C3   0.020
 CF8  plan-1  H1   0.020
 CF8  plan-1  H2   0.020
 CF8  plan-1  H3   0.020
 CF8  plan-1  H4   0.020
 CF8  plan-1  C2   0.020
 CF8  plan-2  C9   0.020
 CF8  plan-2  C10  0.020
 CF8  plan-2  C11  0.020
 CF8  plan-2  C12  0.020
 CF8  plan-2  C13  0.020
 CF8  plan-2  C14  0.020
 CF8  plan-2  C15  0.020
 CF8  plan-2  C16  0.020
 CF8  plan-2  C17  0.020
 CF8  plan-2  C18  0.020
 CF8  plan-2  C19  0.020
 CF8  plan-2  H7   0.020
 CF8  plan-2  H8   0.020
 CF8  plan-2  H9   0.020
 CF8  plan-2  H10  0.020
 CF8  plan-2  H12  0.020
 CF8  plan-2  H13  0.020
 CF8  plan-2  H14  0.020
 CF8  plan-3  C    0.020
 CF8  plan-3  O    0.020
 CF8  plan-3  C1   0.020
 CF8  plan-3  O1   0.020
 CF8  plan-3  H11  0.020
 CF8  plan-4  C    0.020
 CF8  plan-4  C1   0.020
 CF8  plan-4  C3   0.020
 CF8  plan-4  S    0.020
 CF8  plan-4  H15  0.020
 CF8  plan-4  C2   0.020

